major refactoring and update for all the providers.

.codacy.yaml

@@ -0,0 +1,20 @@
+---
+# Codacy configuration. https://docs.codacy.com/repositories-configure/codacy-configuration-file/
+#
+# pydocstyle has two pairs of mutually-exclusive rules:
+#   D203 vs D211 (blank line before class docstring; codebase follows D203)
+#   D212 vs D213 (multi-line summary line; codebase follows D212)
+# Both rules in each pair are enabled in Codacy's default profile, which produces
+# unavoidable noise — pick one and silence the other. Settings here also apply to
+# any local pydocstyle invocation that reads `.pydocstyle`.
+
+engines:
+  pydocstyle:
+    enabled: true
+    settings:
+      add_ignore: ["D211", "D213"]
+
+exclude_paths:
+  - "docs/stylesheets/**"
+  - "docs/plans/**"
+  - "pgatk/tests/**"

.gitignore

@@ -119,7 +119,7 @@ pgatk/config/private/
 # Test-generated output files (produced by pgatk tests)
 pgatk/testdata/proteindb_from_*.fa
 pgatk/testdata/output_decoy.fa
-pgatk/testdata/test_cbioportal_data_mutations_mskcc_proteindb*.fa
+pgatk/testdata/test_cbioportal_*_proteindb*.fa
 pgatk/testdata/test_cosmic_mutations_proteindb*.fa
 pgatk/testdata/test_blast_psms_out.tsv
 pgatk/testdata/test_blast_validate_psms_out.tsv
@@ -135,3 +135,14 @@ pgatk/testdata/Meleagris_gallopavo*
 .DS_Store
 .codacy/
 .cursor/
+
+# Internal working docs (implementation plans, scratch notes)
+docs/plans/
+use-cases/
+# BioPython SeqIO.index_db SQLite indexes — built lazily on first use,
+# rebuilt automatically when the source FASTA changes (mtime check).
+*.fa.idx
+*.fasta.idx
+
+# gffutils / SeqIO SQLite databases — auto-generated, never committed
+pgatk/testdata/*.db

.pydocstyle

@@ -0,0 +1,6 @@
+[pydocstyle]
+# D211 conflicts with D203 (codebase follows D203: one blank line before class docstring).
+# D213 conflicts with D212 (codebase follows D212: multi-line summary on the first line).
+# Disabling the rules we don't follow stops the mutually-exclusive-pair noise from
+# static analysers (pydocstyle, Codacy).
+add-ignore = D211,D213

docs/index.md

@@ -23,6 +23,7 @@ See the [Installation](installation.md) page for more options (Bioconda, Docker,
 | [Introduction](introduction.md) | Overview of the proteogenomics field |
 | [Installation](installation.md) | How to install pgatk (pip, Bioconda, Docker, source) |
 | [pgatk CLI](pgatk-cli.md) | Full command-line reference for all tools |
+| [Validations](validations.md) | Tests and validations to ensure correctness of the modules|
 | [Use Cases](use-cases.md) | End-to-end workflows and recipes for common scenarios |
 | [File Formats](formats.md) | BED, GTF, GCT format specifications |
 | [Changelog](changelog.md) | Version history and release notes |